People

Principal
Investigator

X. Shirley Liu received a PhD in Biomedical Informatics and a PhD minor in Computer Science from Stanford University in 2002. She is a Professor with the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and Harvard School of Public Health. Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

Research
Scientist

Cliff Meyer received his PhD in Chemical Engineering from Princeton University in 2003. He is a computational biologist, with expertise in algorithm development, genomic data integration, cancer gene regulation, epigenetics and nuclear receptor biology. His work includes methodological research projects, collaborative research with experimental biologists, and the broad dissemination of research findings through review articles and software. He has contributed to the development of several widely used algorithms for ChIP-chip, ChIP-seq, MNase-seq, DNase-seq, DNA methylation and CRISPR screen data analysis. Through integrating genome-wide transcription factor binding, chromatin dynamics, and gene expression profiles, he has studied the specificity and function of transcription factors, and chromatin regulators, and has experience in large-scale genomic data integration.

Computational Biologist

Chen-Hao Chen received PhD in Biological and Biomedical Science from Harvard University in 2017. Chen-Hao is a computational biologist with expertise on integrating high dimensional omics data to decipher cancer mechanisms and genome-wide CRISPR-Cas9 knockout screens. He is now developing mathematical framework to model gene regulations.

Data
Scientist

Aashna received her masters in Computer and Information Sciences at the New York University . She is currently working on developing the Bioinformatics Pipelines for CIDC project with other members of the lab.

BIOINFORMATICS ANALYST

David Cohen received his M.S. in Bioinformatics from Northeastern University in late 2017. He is currently working on genomic research with other members of the lab. He has a bioinformatics and data analytics background and is interested in applying cutting edge technology in order to help understand and fight disease.

Programmer

Len Taing received BA and MS in Computer Science from Harvard and MA in Psychological and Brain Sciences from Johns Hopkins. He has been working with the Liu Lab and the Center for Functional Cancer Epigenetics for the last decade, and instrumental to the development of many computational algorithms, pipelines, and databases.

LAB MANAGER

Jin Zhao is originally from Xinjiang, China. She graduated from medical school and worked as a radiation oncologist in China before deciding to move to the United States in 2001. Jin joined the Brown lab in 2005, and working as joint lab manager for Brown and Liu lab in 2015. In her spare time she enjoys crocheting and playing with her dog, Buttons Jr.

EXPERIMENTAL TECHNICIAN

Nicole Traugh received her B.S. in Biology from Saint Michael's College in Colchester, Vermont. She joined the lab as a research technician in 2016, and is interested in cancer immunology, genetics and infectious disease. Her current work involves set up for the in vivo CRISPR screen platform, performing CRISPR screens in vivo and in vitro, as well as working on the interactions between cancer cells and the immune system. She is currently applying to Ph.D. programs in the Boston area, and enjoys reading and cooking spicy food in her spare time.

LAB ASSISTANT

GRANT MANAGER

COMPUTATIONAL POSTDOCS

Dr. Peng Jiangis a postdoc fellow at Xiaole Liu Lab at the Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health. His research focused on developing computational models to identify biomarkers and regulators of anticancer drug resistance, with an application focus on cancer immunotherapies. Peng has many first and co-first authored papers in high profile journals, such as Nature Medicine, Science, and PNAS. He is a recipient of the Pathway to Independence Award (K99/R00) of National Cancer Institute.Peng finished his Ph.D. at the department of computer science and Lewis Sigler genomics institute at Princeton University, and his undergraduate study with the highest honor at the department of computer science at Tsinghua University.

Xihao Hu received PhD in Computer Science from Chinese University of Hong Kong in 2015. He is now a post-doctoral research fellow in Shirley Liu’s laboratory at Dana-Farber Cancer Institute. Sherlock is a computational biologist with expertise on developing statistical models for high-throughput sequencing data and machine learning algorithms for MHC-peptide binding prediction. He is working on integrating three-dimensional protein structures, large-scale genomic data, and deep learning frameworks for understanding antibody-antigen interactions in the tumor microenvironment.

AvinashSahureceived PhD in Computer Science (Computation Biology) from University of Maryland in 2016. He is now a Research fellow at Dana-Farber Cancer Institute and Mass General Hospital, with expertise in a niche that lies in an intersection of deep learning/big data and immuno-oncology. He develops machine learning algorithm to analyze high throughput genomic data to model patient response to cancer drugs.

Collin Tokheimreceived his PhD in Biomedical Engineering from Johns Hopkins University in 2018. During his PhD, his research focused on the development and application ofnovelcomputational methodologiesto statistically implicate mutations underlyingthe development or progression ofhuman cancers.He hasexpertisein machine learning, statisticalmodeling, genomics, and cancer genetics.Collin is now a Research Fellow at the Dana-Farber Cancer Institute.His current research focus is on further dissectingthe process of carcinogenesis, examining the response or resistance of tumors to targeted therapeutics, and analyzing cancer immunology.

Li Song received Ph.D. in Computer Science from Johns Hopkins University in 2018. His research area is on computational biology. He has designed and implemented algorithms to analyze next-generation sequencing data, mostly RNA-seqdata, for various applications, such as transcriptome assembly, error correction, scaffolding, and metagenomics.

Chenfei Wang received PhD in Bioinformatics from Tongji University.He is now aPostdoctoralFellow ofBiostatistics and Computational Biology atHarvard University and Dana-Farber Cancer Institute.During his PhD period he studied the epigenetic reprogramming of mammalian early embryosand somatic nucleartransferred(SCNT)embryosutilizinghigh throughputgenomicdata.Now he is interested in investigating the mechanism of cancer and immune interactions based on single-cell RNA-seq and epigenomic-seq, and focus on utilizing machine learning algorithms to decipherthe regulation ofimmunediversityand cancer progression.

EXPERIMENTAL POSTDOCS

Jingyu Amy Peng received her Ph.D. in Molecular Biology and Biochemistry from Peking University, School of Life Sciences in 2015. She then started her postdoc under the joint supervision of Drs. Myles Brown and X. Shirley Liu. She is an experimental biologist with extensive experience of design and construction of customized single- and paired-guide RNA libraries as well as conducting large-scale CRISPR screens in mammalian systems and also performing mechanistic studies in the fields of oncology and cell biology. She is now focusing on using the CRISPR-based functional genomic study to investigate critical gene interactions and essential regulatory elements like enhancers in breast and prostate cancer models. "

Shengqing Gu received Ph.D. in Medical Biophysics at University of Toronto, where he performed research across two areas under the supervision of Dr. Benjamin Neel: (1) protein tyrosine phosphatase signaling in hematopoiesis, and (2) computational modeling of ovarian cancer clinical course. Stan is currently a postdoctoral fellow co-supervised by Drs. Shirley Liu and Myles Brown. His research combines computational and experimental approaches to interrogate the interaction between cancer cells and the immune system, including (1) identifying new biomarkers for cancer immunotherapy response; (2) elucidating the epigenetic regulation of key components in cancer-T cell interaction; (3) characterizing the immune repertoire in cancer patients and healthy donors.

Qin joined the group in 2017 under co-mentorship of Dr. Myles Brown and Dr. Shirley Liu to study the intricacies of glucocorticoid signaling its impact on the tumor-immune microenvironment, as well as to utilize CRISPR-mediated gene editing to uncover genetic vulnerabilities in glucocorticoid-refractory pediatric leukemia. In her previous academic career as an (almost) cancer researcher, she trained with DavidLangenauat Massachusetts General Hospital to develop immune compromised zebrafish models that allow human and mouse cell transplantation. Qin received her Ph.D. in Human Biology and Translational Medicine from Harvard University in 2017, and B.S. in Biological Sciences from Nanjing University in 2012.

Xiaoqing Wang is a postdoc who received his B.Sc. and M.D. in cardiology from Dalian Medical University in China. His current research is focused on identifying new target proteinwhich can affect proliferation and metastasis of breast cancer by using in vivo genome-wide screening. In his free time, Xiaoqing enjoys auto shows and stamp collecting.

VISITING SCHOLARS

Rongbin Zheng is a visiting PhD student in bioinformatics from Tongji University. He is working onCistromeproject, especially maintaining and updatingCistromeData Browser (http://cistrome.org/db).

Jingxin Fu received abachelor degree in Biotechnologyfrom the Ocean University of China in 2016. She is now a Ph.D. student of bioinformatics at X. Shirley Liu lab in Tongji University, Shanghai, China.Jingxinis a computational biologist with experiences on data integration, visualization, and Web development. Her current research focuses on biomarkers development and evaluation for immunotherapy response. She is also interested in developing microsatellite instability estimation method from the expression profile.

Jin Wang is a PhD candidate in Bioinformatics from Tongji University, Shanghai, China.Jinis interested in cancer immunology, especially exploring cancer-specific immune characteristics from immune repertoire. Currently,Jinis focusedon analyzing BCR repertoire in early lung cancer to identify the relationships between immunoglobulin and cytokines, which helps understand the interaction role of immunoglobulin andcytokines.Sheis also studying tumor-specific CDR3 motifs which can potentially contribute to early lung cancer prognosis.

Jin Wang is a PhD candidate in Bioinformatics from Tongji University, Shanghai, China.Jinis interested in cancer immunology, especially exploring cancer-specific immune characteristics from immune repertoire. Currently,Jinis focusedon analyzing BCR repertoire in early lung cancer to identify the relationships between immunoglobulin and cytokines, which helps understand the interaction role of immunoglobulin andcytokines.Sheis also studying tumor-specific CDR3 motifs which can potentially contribute to early lung cancer prognosis.

Zhe Zhang received a master degree in Obstetrics and Gynaecology from the Chinese PLA general hospital in 2017. He is now an M.D. & Ph.D. student at X. Shirley Liu lab. His main clinical interests include the surgical and medical treatment of women with all types of gynecologic malignancies.His current research focuses on integrating high dimensional omics data to decipher cancer mechanisms and investigating cancer immunotherapy.